Absolutely everyone, apparently, is being persecuted. The religious are being persecuted. Former Archbishop of Canterbury, George Carey, has even seen fit to declare that Christians are being "vilified" and "driven underground". But the non-religious are being persecuted too, according to the National Secular Society — persecuted institutionally by an established system that favours the religious in public life. So, whether you are religious or non-religious, you are not safe. Oh, dear. I think that's everyone, isn't it?

In the latest expression of its long-running beef against the Scout movement, the National Secular Society has written to chief Scout, Bear Grylls, warning that the organisation is excluding atheist children. Goodness! Atheist children [see footnote]. The non-religious can often be heard complaining that people should be allowed to choose their beliefs as adults, rather than be brought up in and on them. Clearly, however, if a child is absolutely certain that God does not exist, then an exception can be made. And that's the root of the trouble, isn't it? If a person agrees with you, then they're a sage. If they don't agree with you, then they're a fool.

Now, I happen to know a lot of Christians. Some of the finest people I know are Christians. But they are all "live and let live" Christians. They tend to understand that sometimes other Christians invite "vilification" because they insist on doing something that doesn't seem very Christian at all. What is it these less palatable Christians do? They insist on persecuting people, that's what.

It wouldn't matter in the least in a world that strove to allow people to believe whatever they wished as much as possible, as long as they afforded others the same compliment. Sure, it's odd that people can believe in God, while not believing in homosexuality or abortion. There is ample evidence that homosexuality and abortion exist, and none at all that God exists. But if people really want to belong to an organisation that insists these things are wrong, then that's up to them. I respect their right to be, in my view, wrong.

The religious people and organisations that will not return that respect, however, are crossing a line. And they will not accept that to cross that line is to invite condemnation, even to revel in it. That's what all the flamboyant campaigning against abortion and homosexuality is about – a refusal to accept that in a free society certain boundaries have to be accepted. If you wish to have no contact with gay people, then this hampers your ability to work with the general public.

If you insist on your right to vilify others, don't be surprised if it comes back and bites you – hard.

But that goes for secular organisations, too. The National Secular Society argues that because joining the Scout movement involves a ceremony in which a child pledges to do his "duty to God", then it is discriminating against children who do not believe in God, or worse, is encouraging them to "lie". Actually, you can perfectly easily do all of your duties to God without believing in God at all – if that's what you want to do. The vast bulk of Christian teaching – indeed the vast bulk of the teachings of all the great religions — happens to be wise, moral and sensible. That's precisely what has attracted millions of humans to them for centuries. If people really don't want their children to be Scouts, then that's their affair. It is for them, in part, that the Woodcraft Folk exists. If it was part of the "duty to God" of a Scout to picket Woodcraft Folk meetings, or campaign for other youth associations to be illegal, then that would be anti-secular. It is not anti-secular to belong to an organisation that has a religious basis or component. It is anti-secular, however, to insist that the law should be partial, imposing one group's idea of what's right when another route can protect individual rights more universally.

Likewise, I completely respect people who believe abortion is wrong. I have no wish to persuade them otherwise. But when they intimidate those whose view is different, or attempt to limit people's ability to access the service, they are behaving very badly indeed.

A pro-life campaigner, Caroline Farrow, kindly took the time to contact me on Twitter this week, to explain that she believed abortion was prevalent precisely because wider society did not respect women, or motherhood. Only by prioritising the reproductive role of women, and properly accommodating it, could female equality be achieved, she believes. Certainly, it would be nice to live in a world in which no woman ever felt the need to terminate a pregnancy. But such a world has never existed. When I asked Farrow to give examples of nations or societies that could help demonstrate a link between lack of access to abortion, and improved gender equality, she offered Ireland and Chile, off the top of her head. Ireland, I discount, as so many women make the journey to Britain and avail themselves of abortion services here. But Chile?

In Chile, abortion is illegal without exception. It also has one of the largest "unexplained gender pay gaps" in the world, according to research released by the International Trade Union Confederation in March. On the other hand, Iceland, where abortion has been legal since 1935, has topped the World Economic Forum's Global Gender Gap rankings for the last two years. In fairness, Chile came in at 42 in the most recent report in 2011, which is not bad at all. However, maternal deaths from illegal abortion suggest that in Chile the dangerous practice of backstreet abortion is rife. And that's the reality. Abortion exists.

That is not one of life's opinions, or beliefs. It is one of life's certainties. Same goes for homosexuality. Same goes for a popular children's organisation that does no harm, and much good, and does not deserve to be targeted and harassed by people wishing to impose their views on everyone. Whenever possible, it is best to accept people as they are, even – especially – when they are not the same as you. Set yourself against that course, and you run the risk of driving all sorts of people "underground", not least among them, yourself.

• This article was amended on 3 October 2012. The original quoted the National Secular Society as using the words "atheist children" in its letter to the Chief Scout, Bear Grylls. It did not use these words but referred to young people who "do not regard themselves as belonging to any religion".